<p>Self-assembly is a promising strategy to develop advanced nanocomposites for state-of-the-art applications. Although self-assembled chitosan/silica nanoparticles could induce tissue regeneration and repair, the research on these materials when used as coatings is scarce and limited to spherical silica nanoparticles. This work reports, for the first time, the alignment of SBA-15 mesoporous silica nanorods (SRs) in coatings prepared by electrophoretic deposition (EPD) of self-assembled chitosan/SRs structures. To exploit the potential applications of the nanocomposites, the relations between their chemical composition, morphology, and microstructure were investigated. Image processing and analysis were used to determine the local orientation of the nanorods, while multivariate statistical analysis and machine learning were conducted on Raman hyperspectral datasets to generate clustering maps representing the spatial distribution of fundamental structural and chemical characteristics such as chitosan deacetylation degree. Besides the presence of acetic acid molecules trapped into the polymeric coating, EPD selectiveness in promoting the deposition of chitosan with high deacetylation degree and low crystallinity was confirmed. Preliminary results of bioactivity and biocompatibility studies are presented, and the acetic acid and chitosan diffusions into simulated body fluid (SBF) are discussed. Chemical and clustering maps indicated that the substrate topography was a crucial factor in the interaction of the organic/inorganic phase with SBF.</p> Graphical abstract <p></p>